# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:29:50 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (1S)-1-(phenoxymethyl)propyl (R)-methylphosphonochloridoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](COc1ccccc1)O[P@](C)(Cl)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 POT  POT  '(1S)-1-(phenoxymethyl)propyl (R)-methylphosphonochloridoate'  ligand  32  16  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_POT
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 POT  P     P   P     0   1.191  4.7218   0.9093   2.8162
 POT  C1    C   CH3   0  -0.925  3.2583   0.4961   1.8724
 POT  O1    O   O     0  -0.657  4.5952   2.0757   3.7157
 POT  O2    O   O2    0  -0.587  5.2681  -0.4413   3.4781
 POT  C2    C   CH1   0  -0.015  4.6615  -0.9678   4.6799
 POT  C3    C   CH2   0  -0.433  4.5904  -2.4757   4.5350
 POT  C4    C   CH3   0  -0.675  3.6753  -2.9311   3.4078
 POT  C5    C   CH2   0  -0.179  5.5259  -0.5022   5.8439
 POT  O3    O   O2    0  -0.478  4.9009  -0.9502   7.0263
 POT  C6    C   CR16  0  -0.241  7.1796   0.2614   9.6337
 POT  C7    C   CR16  0  -0.281  6.5040  -0.1739  10.7621
 POT  C8    C   CR16  0  -0.240  5.3036  -0.8611  10.6085
 POT  C9    C   CR16  0  -0.347  4.7898  -1.1092   9.3480
 POT  C10   C   CR6   0   0.390  5.4751  -0.6676   8.2148
 POT  C11   C   CR16  0  -0.379  6.6762   0.0216   8.3589
 POT  CL1   CL  CL    0  -0.249  6.1696   1.1515   1.4052
 POT  H41   H   HCH3  0   0.224  2.6542  -2.5766   3.5599
 POT  H42   H   HCH3  0   0.227  4.0138  -2.5739   2.4352
 POT  H43   H   HCH3  0   0.243  3.6409  -4.0191   3.3617
 POT  H31   H   HCH2  0   0.247  4.2335  -2.8869   5.4809
 POT  H32   H   HCH2  0   0.235  5.6017  -2.8657   4.3868
 POT  H2    H   HCH1  0   0.249  3.6478  -0.5652   4.8048
 POT  H51   H   HCH2  0   0.234  6.5358  -0.9180   5.7428
 POT  H52   H   HCH2  0   0.245  5.6048   0.5905   5.8365
 POT  H11   H   HCR6  0   0.280  7.2302   0.3770   7.5003
 POT  H7    H   HCR6  0   0.254  6.9036   0.0175  11.7488
 POT  H8    H   HCR6  0   0.258  4.7603  -1.2057  11.4790
 POT  H9    H   HCR6  0   0.262  3.8564  -1.6458   9.2297
 POT  H11A  H   HCH3  0   0.292  3.4300  -0.3570   1.2200
 POT  H12   H   HCH3  0   0.292  2.4437   0.2665   2.5603
 POT  H13   H   HCH3  0   0.303  2.9643   1.3557   1.2722
 POT  H6    H   HCR6  0   0.259  8.1137   0.7991   9.7347

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 POT  P    O2    single    1.600  0.020  1.600
 POT  P    C1    single    1.790  0.020  1.790
 POT  P    O1    double    1.478  0.020  1.478
 POT  P    CL1   single    2.036  0.020  2.036
 POT  C1   H11A  single    0.970  0.020  1.090
 POT  C1   H12   single    0.970  0.020  1.090
 POT  C1   H13   single    0.970  0.020  1.090
 POT  O2   C2    single    1.446  0.020  1.446
 POT  C2   C3    single    1.517  0.020  1.517
 POT  C2   C5    single    1.523  0.020  1.523
 POT  C2   H2    single    0.970  0.020  1.090
 POT  C3   C4    single    1.522  0.020  1.522
 POT  C3   H31   single    0.970  0.020  1.090
 POT  C3   H32   single    0.970  0.020  1.090
 POT  C4   H41   single    0.970  0.020  1.090
 POT  C4   H42   single    0.970  0.020  1.090
 POT  C4   H43   single    0.970  0.020  1.090
 POT  C5   O3    single    1.410  0.020  1.410
 POT  C5   H51   single    0.970  0.020  1.090
 POT  C5   H52   single    0.970  0.020  1.090
 POT  O3   C10   single    1.350  0.020  1.350
 POT  C6   C11   aromatic  1.391  0.020  1.391
 POT  C6   C7    aromatic  1.385  0.020  1.385
 POT  C6   H6    single    0.930  0.020  1.080
 POT  C7   C8    aromatic  1.392  0.020  1.392
 POT  C7   H7    single    0.930  0.020  1.080
 POT  C8   C9    aromatic  1.384  0.020  1.384
 POT  C8   H8    single    0.930  0.020  1.080
 POT  C9   C10   aromatic  1.396  0.020  1.396
 POT  C9   H9    single    0.930  0.020  1.080
 POT  C10  C11   aromatic  1.392  0.020  1.392
 POT  C11  H11   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 POT  CL1   P    O2     98.30  3.000
 POT  CL1   P    O1    112.88  3.000
 POT  O2    P    O1    116.32  3.000
 POT  CL1   P    C1    104.09  3.000
 POT  O1    P    C1    115.65  3.000
 POT  O2    P    C1    107.60  3.000
 POT  H13   C1   H12   108.19  3.000
 POT  H13   C1   H11A  109.34  3.000
 POT  H12   C1   H11A  109.33  3.000
 POT  H13   C1   P     109.22  3.000
 POT  H12   C1   P     109.08  3.000
 POT  H11A  C1   P     111.61  3.000
 POT  C2    O2   P     120.54  3.000
 POT  H2    C2   C5    108.97  3.000
 POT  H2    C2   C3    109.40  3.000
 POT  C5    C2   C3    113.81  3.000
 POT  H2    C2   O2    110.39  3.000
 POT  C5    C2   O2    106.61  3.000
 POT  C3    C2   O2    107.60  3.000
 POT  H32   C3   H31   106.59  3.000
 POT  H32   C3   C4    110.42  3.000
 POT  H31   C3   C4    109.43  3.000
 POT  H32   C3   C2    108.90  3.000
 POT  H31   C3   C2    107.88  3.000
 POT  C4    C3   C2    113.36  3.000
 POT  H43   C4   H42   107.41  3.000
 POT  H43   C4   H41   107.50  3.000
 POT  H42   C4   H41   107.97  3.000
 POT  H43   C4   C3    110.44  3.000
 POT  H42   C4   C3    112.09  3.000
 POT  H41   C4   C3    111.24  3.000
 POT  H52   C5   H51   108.13  3.000
 POT  H52   C5   O3    110.75  3.000
 POT  H51   C5   O3    111.40  3.000
 POT  H52   C5   C2    109.92  3.000
 POT  H51   C5   C2    109.65  3.000
 POT  O3    C5   C2    106.98  3.000
 POT  C10   O3   C5    118.89  3.000
 POT  H6    C6   C11   118.90  3.000
 POT  H6    C6   C7    120.06  3.000
 POT  C11   C6   C7    121.04  3.000
 POT  H7    C7   C8    120.45  3.000
 POT  H7    C7   C6    120.48  3.000
 POT  C8    C7   C6    119.07  3.000
 POT  H8    C8   C9    119.28  3.000
 POT  H8    C8   C7    120.09  3.000
 POT  C9    C8   C7    120.63  3.000
 POT  H9    C9   C10   119.41  3.000
 POT  H9    C9   C8    120.56  3.000
 POT  C10   C9   C8    120.03  3.000
 POT  C11   C10  C9    119.74  3.000
 POT  C11   C10  O3    124.18  3.000
 POT  C9    C10  O3    116.08  3.000
 POT  H11   C11  C10   121.49  3.000
 POT  H11   C11  C6    119.02  3.000
 POT  C10   C11  C6    119.49  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 POT  CONST_01  C9    C10  C11  C6     0.00   0.0  0
 POT  CONST_02  C9    C8   C7   C6     0.00   0.0  0
 POT  CONST_03  C10   C11  C6   C7     0.00   0.0  0
 POT  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 POT  CONST_05  C11   C6   C7   C8     0.00   0.0  0
 POT  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 POT  CONST_07  C8    C9   C10  O3   180.00   0.0  0
 POT  CONST_08  C6    C11  C10  O3   180.00   0.0  0
 POT  CONST_09  H8    C8   C7   C6   180.00   0.0  0
 POT  CONST_10  H11   C11  C6   C7   180.00   0.0  0
 POT  CONST_11  H9    C9   C8   C7   180.00   0.0  0
 POT  CONST_12  H6    C6   C7   C8   180.00   0.0  0
 POT  CONST_13  H7    C7   C8   C9   180.00   0.0  0
 POT  Var_01    C9    C10  O3   C5   178.43  30.0  2
 POT  Var_02    H51   C5   O3   C10   60.02  30.0  1
 POT  Var_03    CL1   P    O2   C2   172.27  30.0  1
 POT  Var_04    H11A  C1   P    O1   178.86  30.0  3
 POT  Var_05    H41   C4   C3   C2   -59.37  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 POT  chir_02  C2  O2  C3  C5   negativ
 POT  chir_03  P   C1  O1  CL1  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 POT  plan-1  O3   0.020
 POT  plan-1  C6   0.020
 POT  plan-1  C7   0.020
 POT  plan-1  C8   0.020
 POT  plan-1  C9   0.020
 POT  plan-1  C10  0.020
 POT  plan-1  C11  0.020
 POT  plan-1  H11  0.020
 POT  plan-1  H7   0.020
 POT  plan-1  H8   0.020
 POT  plan-1  H9   0.020
 POT  plan-1  H6   0.020

